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Conserved domains on  [gi|760139954|ref|WP_043821215|]
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MULTISPECIES: LysR substrate-binding domain-containing protein [Delftia]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 1001158)

LysR family HTH-containing transcriptional regulator

Gene Ontology:  GO:0003677|GO:0003700
PubMed:  19047729

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11139 super family cl32646
DNA-binding transcriptional activator GcvA; Provisional
 1-293 6.17e-56

DNA-binding transcriptional activator GcvA; Provisional


The actual alignment was detected with superfamily member PRK11139:

Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 182.35  E-value: 6.17e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954   1 MRNIPPLHLIAAFDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLHQQTRAPLQAL- 79
Cdd:PRK11139   2 SRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLa 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  80 ETTFGSLVQGRD-VVRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAH-QAPqaplAFHC 157
Cdd:PRK11139  82 EATRKLRARSAKgALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRgNWP----GLRV 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 158 ERLLDDEWFAVAAPRYLEQFEGL----DLAglfrRANLL-SHSRQPWEPWLQAAGLRISAAQRQLSYSDTGFMLDAALNL 232
Cdd:PRK11139 158 EKLLDEYLLPVCSPALLNGGKPLktpeDLA----RHTLLhDDSREDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHG 233

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 760139954 233 QGIALGRRSLVQRLLAERSLVRVSDTAIPCSQSYFLLASERAMVSRHGAAVMDWIRAVAAE 293
Cdd:PRK11139 234 QGVALGNRVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQ 294
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-293 6.17e-56

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 182.35  E-value: 6.17e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954   1 MRNIPPLHLIAAFDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLHQQTRAPLQAL- 79
Cdd:PRK11139   2 SRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLa 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  80 ETTFGSLVQGRD-VVRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAH-QAPqaplAFHC 157
Cdd:PRK11139  82 EATRKLRARSAKgALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRgNWP----GLRV 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 158 ERLLDDEWFAVAAPRYLEQFEGL----DLAglfrRANLL-SHSRQPWEPWLQAAGLRISAAQRQLSYSDTGFMLDAALNL 232
Cdd:PRK11139 158 EKLLDEYLLPVCSPALLNGGKPLktpeDLA----RHTLLhDDSREDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHG 233

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 760139954 233 QGIALGRRSLVQRLLAERSLVRVSDTAIPCSQSYFLLASERAMVSRHGAAVMDWIRAVAAE 293
Cdd:PRK11139 234 QGVALGNRVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQ 294
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
6-293 5.18e-43

DNA-binding transcriptional regulator, LysR family [Transcription];


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 147.71  E-value: 5.18e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954   6 PLHLIAAFDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLHQQTRAPLQALETTFGS 85
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  86 LVQGRD----VVRISALPSFARLRLVPSLTAFQRSHPEVSIAI--DPTTRTVN-LQQGEADIAIRFahqAPQAPLAFHCE 158
Cdd:COG0583   82 LRALRGgprgTLRIGAPPSLARYLLPPLLARFRARHPGVRLELreGNSDRLVDaLLEGELDLAIRL---GPPPDPGLVAR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 159 RLLDDEWFAVAAPRYleqfegldlaglfrranllshsrqpwepwlqaaglriSAAQRQLSYSDTGFMLDAALNLQGIALG 238
Cdd:COG0583  159 PLGEERLVLVASPDH-------------------------------------PLARRAPLVNSLEALLAAVAAGLGIALL 201

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 760139954 239 RRSLVQRLLAERSLVRVSDTAIPCSQSYFLLASERAMVSRHGAAVMDWIRAVAAE 293
Cdd:COG0583  202 PRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 92-287 1.13e-42

The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 145.03  E-value: 1.13e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  92 VVRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAHQAPQAplaFHCERLLDDEWFAVAAP 171
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPG---LEAERLMDEELVPVCSP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 172 RYLEQFEGLDLAGLfRRANLL--SHSRQPWEPWLQAAGLRISAAQRQLSYSDTGFMLDAALNLQGIALGRRSLVQRLLAE 249
Cdd:cd08432   78 ALLAGLPLLSPADL-ARHTLLhdATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAA 156

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 760139954 250 RSLVRVSDTAIPCSQSYFLLASERAMVSRHGAAVMDWI 287
Cdd:cd08432  157 GRLVRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-292 7.36e-20

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 85.42  E-value: 7.36e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954   90 RDVVRISALPSFARLRLVPSLTAFQRSHPEVSIAI--DPTTRTVN-LQQGEADIAIRFahqAPQAPLAFHCERLLDDEWF 166
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELteGNSEELLDlLLEGELDLAIRR---GPPDDPGLEARPLGEEPLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  167 AVAAPRY-LEQFEGLDLAGLFRRANLL----SHSRQPWEPWLQAAGLRIsaaQRQLSYSDTGFMLDAALNLQGIALGRRS 241
Cdd:pfam03466  78 LVAPPDHpLARGEPVSLEDLADEPLILlppgSGLRDLLDRALRAAGLRP---RVVLEVNSLEALLQLVAAGLGIALLPRS 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 760139954  242 LVQRLLAERSLVRVSDTAIPCSQSYFLLASERAMVSRHGAAVMDWIRAVAA 292
Cdd:pfam03466 155 AVARELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 9-91 2.93e-09

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 56.85  E-value: 2.93e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954    9 LIAAFDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRtTRVVTLSAEGAWLHQQTRaPLQALETTFGSLVQ 88
Cdd:TIGR03298   5 QLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHAR-QVRLLEAELLAELP 82


                  ...
gi 760139954   89 GRD 91
Cdd:TIGR03298  83 GLA 85
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-293 6.17e-56

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 182.35  E-value: 6.17e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954   1 MRNIPPLHLIAAFDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLHQQTRAPLQAL- 79
Cdd:PRK11139   2 SRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLa 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  80 ETTFGSLVQGRD-VVRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAH-QAPqaplAFHC 157
Cdd:PRK11139  82 EATRKLRARSAKgALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRgNWP----GLRV 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 158 ERLLDDEWFAVAAPRYLEQFEGL----DLAglfrRANLL-SHSRQPWEPWLQAAGLRISAAQRQLSYSDTGFMLDAALNL 232
Cdd:PRK11139 158 EKLLDEYLLPVCSPALLNGGKPLktpeDLA----RHTLLhDDSREDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHG 233

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 760139954 233 QGIALGRRSLVQRLLAERSLVRVSDTAIPCSQSYFLLASERAMVSRHGAAVMDWIRAVAAE 293
Cdd:PRK11139 234 QGVALGNRVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQ 294
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
13-295 4.39e-44

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 152.08  E-value: 4.39e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  13 FDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLhqqtrapLQALETTFGSLVQG-RD 91
Cdd:PRK10086  22 FEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRV-------FWALKSSLDTLNQEiLD 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  92 V--------VRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAHqAPQAPLafHCERLLDD 163
Cdd:PRK10086  95 IknqelsgtLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDD-APSAQL--THHFLMDE 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 164 EWFAVAAPRYLEQFeglDLAGlfRRANL----LSHSRQP---------WEPWLQAAGLRISAAQRQLSYSDTGFMLDAAL 230
Cdd:PRK10086 172 EILPVCSPEYAERH---ALTG--NPDNLrhctLLHDRQAwsndsgtdeWHSWAQHFGVNLLPPSSGIGFDRSDLAVIAAM 246

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 760139954 231 NLQGIALGRRSLVQRLLAERSLVR-VSDTAIPCSQSYFLlaseramVSRHGA------AVMDWIRAVAAEAG 295
Cdd:PRK10086 247 NHIGVAMGRKRLVQKRLASGELVApFGDMEVKCHQHYYV-------TTLPGRqwpkieAFIDWLKEQVKTTS 311
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
6-293 5.18e-43

DNA-binding transcriptional regulator, LysR family [Transcription];


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 147.71  E-value: 5.18e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954   6 PLHLIAAFDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLHQQTRAPLQALETTFGS 85
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  86 LVQGRD----VVRISALPSFARLRLVPSLTAFQRSHPEVSIAI--DPTTRTVN-LQQGEADIAIRFahqAPQAPLAFHCE 158
Cdd:COG0583   82 LRALRGgprgTLRIGAPPSLARYLLPPLLARFRARHPGVRLELreGNSDRLVDaLLEGELDLAIRL---GPPPDPGLVAR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 159 RLLDDEWFAVAAPRYleqfegldlaglfrranllshsrqpwepwlqaaglriSAAQRQLSYSDTGFMLDAALNLQGIALG 238
Cdd:COG0583  159 PLGEERLVLVASPDH-------------------------------------PLARRAPLVNSLEALLAAVAAGLGIALL 201

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 760139954 239 RRSLVQRLLAERSLVRVSDTAIPCSQSYFLLASERAMVSRHGAAVMDWIRAVAAE 293
Cdd:COG0583  202 PRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 92-287 1.13e-42

The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 145.03  E-value: 1.13e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  92 VVRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAHQAPQAplaFHCERLLDDEWFAVAAP 171
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPG---LEAERLMDEELVPVCSP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 172 RYLEQFEGLDLAGLfRRANLL--SHSRQPWEPWLQAAGLRISAAQRQLSYSDTGFMLDAALNLQGIALGRRSLVQRLLAE 249
Cdd:cd08432   78 ALLAGLPLLSPADL-ARHTLLhdATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAA 156

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 760139954 250 RSLVRVSDTAIPCSQSYFLLASERAMVSRHGAAVMDWI 287
Cdd:cd08432  157 GRLVRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-292 7.36e-20

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 85.42  E-value: 7.36e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954   90 RDVVRISALPSFARLRLVPSLTAFQRSHPEVSIAI--DPTTRTVN-LQQGEADIAIRFahqAPQAPLAFHCERLLDDEWF 166
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELteGNSEELLDlLLEGELDLAIRR---GPPDDPGLEARPLGEEPLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  167 AVAAPRY-LEQFEGLDLAGLFRRANLL----SHSRQPWEPWLQAAGLRIsaaQRQLSYSDTGFMLDAALNLQGIALGRRS 241
Cdd:pfam03466  78 LVAPPDHpLARGEPVSLEDLADEPLILlppgSGLRDLLDRALRAAGLRP---RVVLEVNSLEALLQLVAAGLGIALLPRS 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 760139954  242 LVQRLLAERSLVRVSDTAIPCSQSYFLLASERAMVSRHGAAVMDWIRAVAA 292
Cdd:pfam03466 155 AVARELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 95-287 7.26e-19

The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 82.34  E-value: 7.26e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  95 ISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAHQA-PQAplafHCERLLDDEWFAVAAPRY 173
Cdd:cd08481    4 LAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVwPGA----ESEYLMDEEVVPVCSPAL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 174 LEQFEGLDLAGLFrRANLLSHSRQP--WEPWLQAAGLRISAAQRQLSYSDTGFMLDAALNLQGIALGRRSLVQRLLAERS 251
Cdd:cd08481   80 LAGRALAAPADLA-HLPLLQQTTRPeaWRDWFEEVGLEVPTAYRGMRFEQFSMLAQAAVAGLGVALLPRFLIEEELARGR 158

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 760139954 252 LVRVSDTAIPCSQSYFLLASERAMVSRHGAAVMDWI 287
Cdd:cd08481  159 LVVPFNLPLTSDKAYYLVYPEDKAESPPVQAFRDWL 194
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 92-255 1.45e-18

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 81.72  E-value: 1.45e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  92 VVRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAHQAPQaplAFHCERLLDDEWFAVAAP 171
Cdd:cd08422    2 RLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDS---SLVARRLGPVRRVLVASP 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 172 RYLEQFeGL-----DLAGLfrraNLLSHSR-QPWEPW-LQAAGLRIS-AAQRQLSYSDTGFMLDAALNLQGIALGRRSLV 243
Cdd:cd08422   79 AYLARH-GTpqtpeDLARH----RCLGYRLpGRPLRWrFRRGGGEVEvRVRGRLVVNDGEALRAAALAGLGIALLPDFLV 153

                        170
                 ....*....|..
gi 760139954 244 QRLLAERSLVRV 255
Cdd:cd08422  154 AEDLASGRLVRV 165
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-65 3.21e-18

Bacterial regulatory helix-turn-helix protein, lysR family;


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 76.65  E-value: 3.21e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 760139954    7 LHLIAAFDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEG 65
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK09986 PRK09986
LysR family transcriptional regulator;
7-185 1.29e-14

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 72.45  E-value: 1.29e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954   7 LHLIAAFDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLHQQTRAPLQALETTFGSL 86
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARV 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  87 VQ------GRDVVRISALPSFARLRlvPSLTAFQRSHPEVSIAID---PTTRTVNLQQGEADIAI-RFAhqAPQAPLAFH 156
Cdd:PRK09986  89 EQigrgeaGRIEIGIVGTALWGRLR--PAMRHFLKENPNVEWLLRelsPSMQMAALERRELDAGIwRMA--DLEPNPGFT 164

                        170       180       190
                 ....*....|....*....|....*....|.
gi 760139954 157 CeRLLDDEWFAVAAPR--YLEQFEGLDLAGL 185
Cdd:PRK09986 165 S-RRLHESAFAVAVPEehPLASRSSVPLKAL 194
PRK09801 PRK09801
LysR family transcriptional regulator;
16-255 1.97e-14

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 72.38  E-value: 1.97e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  16 VARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLHQQTRAPLQALETTFGSLVQGRD---- 91
Cdd:PRK09801  17 IVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQIKTrpeg 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  92 VVRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAHQAPQAPLAfhcERLLDDEWFAVAAP 171
Cdd:PRK09801  97 MIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIA---HLLTKNKRILCAAP 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 172 RYLEQF-EGLDLAGLFRRANLLSHSRQP----WE--PWLQAAGLRISAaqrQLSYSDTGFMLDAALNLQGIALGRRSLVQ 244
Cdd:PRK09801 174 EYLQKYpQPQSLQELSRHDCLVTKERDMthgiWElgNGQEKKSVKVSG---HLSSNSGEIVLQWALEGKGIMLRSEWDVL 250

                        250
                 ....*....|.
gi 760139954 245 RLLAERSLVRV 255
Cdd:PRK09801 251 PFLESGKLVQV 261
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
10-93 6.40e-14

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 70.61  E-value: 6.40e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  10 IAAFDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLHQQTRAPLQALETTFGSLVQG 89
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQV 86


                 ....
gi 760139954  90 RDVV 93
Cdd:PRK10094  87 NDGV 90
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
13-170 3.15e-13

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 68.54  E-value: 3.15e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  13 FDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLHQQTRAPLQALETTFGSLVQGRDV 92
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGSDY 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  93 ----VRISALPSFArLRLVPSLTAFQRSHPEVSI-AIDPTTRTVNLQQGEADIAIRFAHQ-APQAPlaFHCERLLDDEWF 166
Cdd:PRK10082  99 aqrkIKIAAAHSLS-LGLLPSIISQMPPLFTWAIeAIDVDEAVDKLREGQSDCIFSFHDEdLLEAP--FDHIRLFESQLF 175


                 ....
gi 760139954 167 AVAA 170
Cdd:PRK10082 176 PVCA 179
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 93-244 5.68e-13

The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold; The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176172 [Multi-domain]  Cd Length: 190  Bit Score: 66.21  E-value: 5.68e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  93 VRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAHQA-PQAplafHCERLLDDEWFAVAAP 171
Cdd:cd08483    2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDwPGL----ESEPLTAAPFVVVAAP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 172 RYLEQFEGLDLAGLFRranllshsrqpwEPWLQAAG---LRISAAQRQLSYSDTGF--------MLDAALNLQGIALGRR 240
Cdd:cd08483   78 GLLGDRKVDSLADLAG------------LPWLQERGtneQRVWLASMGVVPDLERGvtflpgqlVLEAARAGLGLSIQAR 145


                 ....
gi 760139954 241 SLVQ 244
Cdd:cd08483  146 ALVE 149
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 10-152 2.85e-12

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 65.75  E-value: 2.85e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  10 IAAFDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEG-AWLHQQTRApLQALETTFGSL-- 86
Cdd:PRK11242   6 IRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGeVYLRYARRA-LQDLEAGRRAIhd 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 760139954  87 VQ--GRDVVRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTR---TVNLQQGEADIAIRFAhqAPQAP 152
Cdd:PRK11242  85 VAdlSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQeriEALLADDELDVGIAFA--PVHSP 153
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 14-82 9.79e-12

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 64.19  E-value: 9.79e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 760139954  14 DAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLHQQTRAPLQALETT 82
Cdd:PRK11074  11 DAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQET 79
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 13-141 1.75e-11

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 63.64  E-value: 1.75e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  13 FDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLHQQTRAPLQALETTFG---SLVQG 89
Cdd:PRK09906   9 FVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLrarKIVQE 88

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 760139954  90 RDVVRISALPSfARLRLVPS-LTAFQRSHPEVSI---AIDPTTRTVNLQQGEADIA 141
Cdd:PRK09906  89 DRQLTIGFVPS-AEVNLLPKvLPMFRLRHPDTLIelvSLITTQQEEKLRRGELDVG 143
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 5-143 2.53e-11

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 63.09  E-value: 2.53e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954   5 PPLHLIAAFDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLHQQTRAPL---QALET 81
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLveaQAAQD 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 760139954  82 TFGSL-VQGRDVVRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIR 143
Cdd:PRK14997  82 AIAALqVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIR 144
PRK09791 PRK09791
LysR family transcriptional regulator;
7-171 3.64e-11

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 62.47  E-value: 3.64e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954   7 LHLIAAFDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLHQQTRAPLQAL----ETT 82
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELraaqEDI 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  83 FGSLVQGRDVVRISALPSFARLRLVPSLTAFQRSHPEVSIAI---DPTTRTVNLQQGEADIAIRFAHQAP-QAPLAFhcE 158
Cdd:PRK09791  87 RQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRImegQLVSMINELRQGELDFTINTYYQGPyDHEFTF--E 164

                        170
                 ....*....|...
gi 760139954 159 RLLDDEWFAVAAP 171
Cdd:PRK09791 165 KLLEKQFAVFCRP 177
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-287 1.60e-10

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176161  Cd Length: 202  Bit Score: 59.45  E-value: 1.60e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  93 VRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAHQAPQAPLAfhcERLLDDEWFAVAAPR 172
Cdd:cd08472    3 LRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVA---RRLGELRMVTCASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 173 YLEQFeGL-----DLAGlFRRANLLSHS---RQPWEpWLQAAGLRISAAQRQLSYSDTGFMLDAALNLQGIALGRRSLVQ 244
Cdd:cd08472   80 YLARH-GTprhpeDLER-HRAVGYFSARtgrVLPWE-FQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVR 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 760139954 245 RLLAERSLVRVSDTAIPCSQSYFLLASERAMVSRHGAAVMDWI 287
Cdd:cd08472  157 PHLASGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVRVFVDWV 199
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 95-253 1.96e-10

The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is involved in control of tryptophan synthesis, contains type 2 periplasmic binding fold; TrpI and indoleglycerol phosphate (InGP), are required to activate transcription of the trpBA, the genes for tryptophan synthase. The trpBA is induced by the InGp substrate, rather than by tryptophan, but the exact mechanism of the activation event is not known. This substrate-binding domain of TrpI shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176171 [Multi-domain]  Cd Length: 195  Bit Score: 58.95  E-value: 1.96e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  95 ISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAhqAPQAPLAFHCERLLDDEWFAVAAPRYL 174
Cdd:cd08482    4 LSCSGSLLMRWLIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFN--DAPWPAGMQVIELFPERVGPVCSPSLA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 175 -EQFEGLDLAGLFRRANLLSHSRQP--WEPWLQAAGLRISAAQRQLSYSDTGFMLDAALNLQGIALGRRSLVQRLLAERS 251
Cdd:cd08482   82 pTVPLRQAPAAALLGAPLLHTRSRPqaWPDWAAAQGLAPEKLGTGQSFEHFYYLLEAAVAGLGVAIAPWPLVRDDLASGR 161


                 ..
gi 760139954 252 LV 253
Cdd:cd08482  162 LV 163
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 92-287 2.93e-10

The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold; AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176177 [Multi-domain]  Cd Length: 191  Bit Score: 58.31  E-value: 2.93e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  92 VVRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAHQAPQAPLAFhceRLLDDEWFAVAAP 171
Cdd:cd08488    1 VLHVGAVGTFAVGWLLPRLADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDAT---RLFEAPLSPLCTP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 172 RYLEQFEglDLAGLFRRANLLSHSRQPWEPWLQAAGLRISAAQRQLSYSDTGF-MLDAALNLQGIALGRRSLVQRLLAER 250
Cdd:cd08488   78 ELARQLR--EPADLARHTLLRSYRADEWPQWFEAAGVGHPCGLPNSIMFDSSLgMMEAALQGLGVALAPPSMFSRQLASG 155

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 760139954 251 SLVRVSDTAIPCSqSYFLLASERAMVSRHGAAVMDWI 287
Cdd:cd08488  156 ALVQPFATTLSTG-SYWLTRLQSRPETPAMSAFSAWL 191
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-275 3.59e-10

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176166  Cd Length: 197  Bit Score: 58.40  E-value: 3.59e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  92 VVRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFahqAPQAPLAFHCERLLDDEWFAVAAP 171
Cdd:cd08477    2 KLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRI---GELADSSLVARPLAPYRMVLCASP 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 172 RYLEQFEGL----DLAglfrRANLLSHS----RQPWEpwLQAAGLRISAAQR-QLSYSDTGFMLDAALNLQGIALGRRSL 242
Cdd:cd08477   79 DYLARHGTPttpeDLA----RHECLGFSywraRNRWR--LEGPGGEVKVPVSgRLTVNSGQALRVAALAGLGIVLQPEAL 152

                        170       180       190
                 ....*....|....*....|....*....|....
gi 760139954 243 VQRLLAERSLVRV-SDTAIPCSQSYFLLASERAM 275
Cdd:cd08477  153 LAEDLASGRLVELlPDYLPPPRPMHLLYPPDRRP 186
rbcR CHL00180
LysR transcriptional regulator; Provisional
 13-142 1.27e-09

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 58.11  E-value: 1.27e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  13 FDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLHQQTRAPLQALETTFGSLVQGRDV 92
Cdd:CHL00180  13 LKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDLKNL 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 760139954  93 VR----ISALPSFARLrLVPSLTA-FQRSHPEVSIAID-PTTRTV--NLQQGEADIAI 142
Cdd:CHL00180  93 QRgtliIGASQTTGTY-LMPRLIGlFRQRYPQINVQLQvHSTRRIawNVANGQIDIAI 149
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
9-80 2.47e-09

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 57.09  E-value: 2.47e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 760139954   9 LIAAFDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRtTRVVTLSAEGAWLHQQTRaPLQALE 80
Cdd:PRK03635   6 QLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHAR-QVRLLE 75
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-255 2.70e-09

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 55.93  E-value: 2.70e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  93 VRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAHQAPQAPLAFhceRLLDD-EWFAVAAP 171
Cdd:cd08474    5 LRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAV---PLGPPlRMAVVASP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 172 RYLEQFeGL-----DLAG----LFRRANllSHSRQPWEpwLQAAGLRIS-AAQRQLSYSDTGFMLDAALNLQGIALGRRS 241
Cdd:cd08474   82 AYLARH-GTpehprDLLNhrciRYRFPT--SGALYRWE--FERGGRELEvDVEGPLILNDSDLMLDAALDGLGIAYLFED 156

                        170
                 ....*....|....
gi 760139954 242 LVQRLLAERSLVRV 255
Cdd:cd08474  157 LVAEHLASGRLVRV 170
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 9-91 2.93e-09

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 56.85  E-value: 2.93e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954    9 LIAAFDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRtTRVVTLSAEGAWLHQQTRaPLQALETTFGSLVQ 88
Cdd:TIGR03298   5 QLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHAR-QVRLLEAELLAELP 82


                  ...
gi 760139954   89 GRD 91
Cdd:TIGR03298  83 GLA 85
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 93-250 4.76e-09

The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, oxidative stress responses, nodule formation of nitrogen-fixing bacteria, synthesis of virulence factors, toxin production, attachment and secretion, to name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 54.91  E-value: 4.76e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  93 VRISALPSFARLRLVPSLTAFQRSHPEVSIAI--DPTTRTVN-LQQGEADIAIRFahqAPQAPLAFHCERLLDDEWFAVA 169
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLveGGSSELLEaLLEGELDLAIVA---LPVDDPGLESEPLFEEPLVLVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 170 APRY---------LEQFEGLDLAgLFRRAnllSHSRQPWEPWLQAAGLRIsaaQRQLSYSDTGFMLDAALNLQGIALGRR 240
Cdd:cd05466   79 PPDHplakrksvtLADLADEPLI-LFERG---SGLRRLLDRAFAEAGFTP---NIALEVDSLEAIKALVAAGLGIALLPE 151

                        170
                 ....*....|
gi 760139954 241 SLVQRLLAER 250
Cdd:cd05466  152 SAVEELADGG 161
PRK10341 PRK10341
transcriptional regulator TdcA;
8-169 5.30e-09

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 56.02  E-value: 5.30e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954   8 HLIAaFDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLHQQTRAPLQALETTFGSL- 86
Cdd:PRK10341  11 HLVV-FQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIn 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  87 -VQGRDVVRIS-ALPSFARLRLVPS-LTAFQRSHPEVSIAID--------PTTRTvnlqqGEADIAIRfAHQAPQAPLAF 155
Cdd:PRK10341  90 gMSSEAVVDVSfGFPSLIGFTFMSDmINKFKEVFPKAQVSMYeaqlssflPAIRD-----GRLDFAIG-TLSNEMKLQDL 163

                        170
                 ....*....|....
gi 760139954 156 HCERLLDDEWFAVA 169
Cdd:PRK10341 164 HVEPLFESEFVLVA 177
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-255 9.36e-09

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 9. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176168 [Multi-domain]  Cd Length: 198  Bit Score: 54.14  E-value: 9.36e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  94 RISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAhqAPQAPLaFHCERLLDDEWFAVAAPRY 173
Cdd:cd08479    4 RVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVG--DLPDSS-LIARKLAPNRRILCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 174 LEQFEGL----DLAG---LFRRANLLSHSRQPWEPWLQAAGLRISAAqrqLSYSDTGFMLDAALNLQGIALgrRSL--VQ 244
Cdd:cd08479   81 LERHGAPaspeDLARhdcLVIRENDEDFGLWRLRNGDGEATVRVRGA---LSSNDGEVVLQWALDGHGIIL--RSEwdVA 155

                        170
                 ....*....|.
gi 760139954 245 RLLAERSLVRV 255
Cdd:cd08479  156 PYLRSGRLVRV 166
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
11-58 1.78e-08

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 54.59  E-value: 1.78e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 760139954  11 AAFDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRV 58
Cdd:PRK13348   8 EALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRPC 55
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 92-260 4.37e-08

The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 51.99  E-value: 4.37e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  92 VVRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAHQAPQAPLAfhcERLLDDEWFAVAAP 171
Cdd:cd08484    1 VLTVGAVGTFAVGWLLPRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDA---TRLFEAPLSPLCTP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 172 RYLEQF-EGLDLAglfrRANLL-SHSRQPWEPWLQAAGLRISAAQRQLSYSDTGfMLDAALNLQGIALGRRSLVQRLLAE 249
Cdd:cd08484   78 ELARRLsEPADLA----NETLLrSYRADEWPQWFEAAGVPPPPINGPVFDSSLL-MVEAALQGAGVALAPPSMFSRELAS 152

                        170
                 ....*....|.
gi 760139954 250 RSLVRVSDTAI 260
Cdd:cd08484  153 GALVQPFKITV 163
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 92-260 1.14e-07

The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold; This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176176 [Multi-domain]  Cd Length: 189  Bit Score: 51.01  E-value: 1.14e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  92 VVRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAHQAPQAPLAfhcERLLDDEWFAVAAP 171
Cdd:cd08487    1 VLTVGAVGTFAVGWLLPRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEGLWPATHN---ERLLDAPLSVLCSP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 172 RYLEQF-EGLDLAG--LFRranllSHSRQPWEPWLQAAGLRISAAqRQLSYSDTGFMLDAALNLQGIALGRRSLVQRLLA 248
Cdd:cd08487   78 EIAKRLsHPADLINetLLR-----SYRTDEWLQWFEAANMPPIKI-RGPVFDSSRLMVEAAMQGAGVALAPAKMFSREIE 151

                        170
                 ....*....|..
gi 760139954 249 ERSLVRVSDTAI 260
Cdd:cd08487  152 NGQLVQPFKIEV 163
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-175 1.31e-07

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 10. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176169  Cd Length: 198  Bit Score: 50.80  E-value: 1.31e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  93 VRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAHQAPQAPLAfhcERLLDDEWFAVAAPR 172
Cdd:cd08480    3 LRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVA---RKLGESRRVIVASPS 79


                 ...
gi 760139954 173 YLE 175
Cdd:cd08480   80 YLA 82
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
30-156 1.49e-07

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 51.36  E-value: 1.49e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  30 NLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLH---QQTRAPLQALETtfgSLVQGRDVVRisalpsfARLRL 106
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRpfaQQTLLQWQQLRH---TLDQQGPSLS-------GELSL 71

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 760139954 107 VPSLTA-----------FQRSHPEVSIAI---DPTTRTVNLQQGEADIAIRFAHQAPQAPLAFH 156
Cdd:PRK11716  72 FCSVTAayshlppildrFRAEHPLVEIKLttgDAADAVEKVQSGEADLAIAAKPETLPASVAFS 135
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-255 3.74e-07

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176164 [Multi-domain]  Cd Length: 199  Bit Score: 49.48  E-value: 3.74e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  93 VRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAHQAPQAPLAfhcERLLDDEWFAV-AAP 171
Cdd:cd08475    3 LRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGELADSTGLV---ARRLGTQRMVLcASP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 172 RYLEQF-EGLDLAGLFRRANLLSHSRQPWEPWL----QAAGLRISAAQRqLSYSDTGFMLDAALNLQGIALGRRSLVQRL 246
Cdd:cd08475   80 AYLARHgTPRTLEDLAEHQCIAYGRGGQPLPWRladeQGRLVRFRPAPR-LQFDDGEAIADAALAGLGIAQLPTWLVADH 158


                 ....*....
gi 760139954 247 LAERSLVRV 255
Cdd:cd08475  159 LQRGELVEV 167
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
9-65 7.31e-07

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 49.63  E-value: 7.31e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 760139954   9 LIAAFDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEG 65
Cdd:PRK03601   5 LLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAG 61
PRK11482 PRK11482
DNA-binding transcriptional regulator;
1-142 1.17e-06

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 48.95  E-value: 1.17e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954   1 MRNIPpLHLIAAFDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLH----QQTRAPL 76
Cdd:PRK11482  26 LRNID-LNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHeyisQGLESIL 104

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 760139954  77 QALETTfGSLVQGRdVVRISALPSFARLRLVPSLTAFQRSHPEV---SIAIDPTTRtvNLQQGEADIAI 142
Cdd:PRK11482 105 GALDIT-GSYDKQR-TITIATTPSVGALVMPVIYQAIKTHYPQLllrNIPISDAEN--QLSQFQTDLII 169
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 14-142 1.92e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 48.50  E-value: 1.92e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  14 DAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRT-TRVVTLSAEGAWLHQQT-RAPLQA-----LETTFGSL 86
Cdd:PRK12683  11 EAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPGKELLQIVeRMLLDAenlrrLAEQFADR 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 760139954  87 VQGRDVvrISALPSFARLRLVPSLTAFQRSHPEVSIAI---DPTTRTVNLQQGEADIAI 142
Cdd:PRK12683  91 DSGHLT--VATTHTQARYALPKVVRQFKEVFPKVHLALrqgSPQEIAEMLLNGEADIGI 147
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-276 8.09e-06

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 4. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176162 [Multi-domain]  Cd Length: 202  Bit Score: 45.62  E-value: 8.09e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  90 RDVVRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAHQAPQA------PLAFHCERLldd 163
Cdd:cd08473    2 RGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVRFPPLEDsslvmrVLGQSRQRL--- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 164 ewfaVAAPRYLEQF----EGLDLAGLFRRANLLSHSRQPWEpwLQAA-GLRISAAQR-QLSYSDTGFMLDAALNLQGIAL 237
Cdd:cd08473   79 ----VASPALLARLgrprSPEDLAGLPTLSLGDVDGRHSWR--LEGPdGESITVRHRpRLVTDDLLTLRQAALAGVGIAL 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 760139954 238 GRRSLVQRLLAERSLVRV-SDTAIPCSQSYFLLASERAMV 276
Cdd:cd08473  153 LPDHLCREALRAGRLVRVlPDWTPPRGIVHAVFPSRRGLL 192
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 7-68 1.16e-05

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 46.17  E-value: 1.16e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 760139954   7 LHLIAAFDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWL 68
Cdd:PRK15092  13 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQL 74
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-177 1.82e-05

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176159  Cd Length: 197  Bit Score: 44.61  E-value: 1.82e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  93 VRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAHQAPQAPLAfhcERLLDDEWFAVAAPR 172
Cdd:cd08470    3 LRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMA---RRLASRRHYVCASPA 79


                 ....*
gi 760139954 173 YLEQF 177
Cdd:cd08470   80 YLERH 84
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
24-142 2.09e-05

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 45.35  E-value: 2.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  24 QAAEELNLSDSAVSHRIRELEKLLGTPLFHRT-TRVVTLSAEGAWLHQQTRAPLQALET------TFGSLVQGRDVvrIS 96
Cdd:PRK12684  21 EAAKALYTSQPGVSKAIIELEDELGVEIFTRHgKRLRGLTEPGRIILASVERILQEVENlkrvgkEFAAQDQGNLT--IA 98

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 760139954  97 ALPSFARLRLVPSLTAFQRSHPEVSIAI---DPTTRTVNLQQGEADIAI 142
Cdd:PRK12684  99 TTHTQARYALPAAIKEFKKRYPKVRLSIlqgSPTQIAEMVLHGQADLAI 147
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-171 4.71e-05

TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 43.28  E-value: 4.71e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  93 VRISALPSFARLRLVPSLTAFQRSHPEVSIAI--DPTTRTVN-LQQGEADIAIRFahqAPQAPLAFHCERLLDDEWFAVA 169
Cdd:cd08440    2 VRVAALPSLAATLLPPVLAAFRRRHPGIRVRLrdVSAEQVIEaVRSGEVDFGIGS---EPEADPDLEFEPLLRDPFVLVC 78


                 ..
gi 760139954 170 AP 171
Cdd:cd08440   79 PK 80
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 13-119 5.50e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 43.91  E-value: 5.50e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  13 FDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLHQQTRAPL-QALETTfgSLVQGRD 91
Cdd:PRK10837  11 FAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLeQAVEIE--QLFREDN 88

                         90       100
                 ....*....|....*....|....*....
gi 760139954  92 -VVRISALPSFARLRLVPSLTAFQRSHPE 119
Cdd:PRK10837  89 gALRIYASSTIGNYILPAMIARYRRDYPQ 117
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 15-76 9.85e-05

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 43.09  E-value: 9.85e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 760139954  15 AVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLHQQTRAPL 76
Cdd:PRK11151  11 ALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVL 72
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
15-173 1.80e-04

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 42.31  E-value: 1.80e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  15 AVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLHQQTRAPLQALETTFGSLVQgrdvvr 94
Cdd:PRK15421  12 ALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACNE------ 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  95 isalPSFARLR-----------LVPSLTAFQRSHPEVS------IAIDPTTrtvNLQQGEADIAIRfAHQAPQAPLafHC 157
Cdd:PRK15421  86 ----PQQTRLRiaiechsciqwLTPALENFHKNWPQVEmdfksgVTFDPQP---ALQQGELDLVMT-SDILPRSGL--HY 155

                        170
                 ....*....|....*.
gi 760139954 158 ERLLDDEWFAVAAPRY 173
Cdd:PRK15421 156 SPMFDYEVRLVLAPDH 171
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-258 5.19e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176165  Cd Length: 197  Bit Score: 40.31  E-value: 5.19e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  94 RISaLPSFARLrLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFAHqAPQAPLA------FHceRLLddewfa 167
Cdd:cd08476    4 RVS-LPLVGGL-LLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGE-LPDSRLMsrrlgsFR--MVL------ 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954 168 VAAPRYLEQfegldlAGLFRR-ANLLSHS----RQP----WEPW-LQAAGLRISAAQRQLSYSDTG-FMLDAALNLQGIA 236
Cdd:cd08476   73 VASPDYLAR------HGTPETpADLAEHAclryRFPttgkLEPWpLRGDGGDPELRLPTALVCNNIeALIEFALQGLGIA 146

                        170       180
                 ....*....|....*....|..
gi 760139954 237 LGRRSLVQRLLAERSLVRVSDT 258
Cdd:cd08476  147 CLPDFSVREALADGRLVTVLDD 168
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
7-77 1.55e-03

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 39.36  E-value: 1.55e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 760139954   7 LHLIAAFDAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLFHRTTRVVTLSAEGAWLHQQTRAPLQ 77
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLH 74
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-172 3.84e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 37.58  E-value: 3.84e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  93 VRISALPSFARLRLVPSLTAFQRSHPEVSIA---IDPTTRTVNLQQGEADIAIRFAHQAPQAPLA--FHCERLLDDEwFA 167
Cdd:cd08423    2 LRVGAFPTAAAALLPPALAALRARHPGLEVRlreAEPPESLDALRAGELDLAVVFDYPVTPPPDDpgLTRVPLLDDP-LD 80


                 ....*
gi 760139954 168 VAAPR 172
Cdd:cd08423   81 LVLPA 85
cbl PRK12679
HTH-type transcriptional regulator Cbl;
14-142 5.89e-03

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 37.87  E-value: 5.89e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  14 DAVARSQSFKQAAEELNLSDSAVSHRIRELEKLLGTPLF-HRTTRVVTLSAEG-AWLHQQTRAPLQA-----LETTFGSL 86
Cdd:PRK12679  11 EAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFiRRGKRLLGMTEPGkALLVIAERILNEAsnvrrLADLFTND 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 760139954  87 VQGrdVVRISALPSFARLRLVPSLTAFQRSHPEVSIAI---DPTTRTVNLQQGEADIAI 142
Cdd:PRK12679  91 TSG--VLTIATTHTQARYSLPEVIKAFRELFPEVRLELiqgTPQEIATLLQNGEADIGI 147
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 90-175 8.24e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain; This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 36.55  E-value: 8.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 760139954  90 RDVVRISALPSFARLRLVPSLTAFQRSHPEVSIAIDPTTRTVNLQQGEADIAIRFahqAPQAPLAFHCERLLDDEWFAVA 169
Cdd:cd08478    2 SGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRI---GELTDSTLHARPLGKSRLRILA 78


                 ....*.
gi 760139954 170 APRYLE 175
Cdd:cd08478   79 SPDYLA 84
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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